public interface PeptideMapper
Modifier and Type | Method and Description |
---|---|
void |
close()
Closes all connections to files, tries to delete corrupted and deprecated
indexes.
|
void |
emptyCache()
Empties all caches.
|
ArrayList<PeptideProteinMapping> |
getProteinMapping(String peptideSequence,
SequenceMatchingPreferences proteinInferencePreferences)
Returns the protein mapping in the FASTA file loaded in the sequence
factory for the given peptide sequence in a map: peptide sequence found
in the FASTA file | protein accession | list of indexes of the peptide
sequence on the protein sequence.
|
ArrayList<PeptideProteinMapping> |
getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the protein mappings for the given peptide sequence.
|
ArrayList<PeptideProteinMapping> |
getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance)
Returns the protein mappings for the given peptide sequence.
|
ArrayList<PeptideProteinMapping> getProteinMapping(String peptideSequence, SequenceMatchingPreferences proteinInferencePreferences) throws IOException, InterruptedException, ClassNotFoundException, SQLException
peptideSequence
- the peptide sequenceproteinInferencePreferences
- the sequence matching preferencesIOException
- exception thrown whenever an error occurs while
reading or writing a fileClassNotFoundException
- exception thrown whenever an error occurs
while deserializing an objectInterruptedException
- exception thrown whenever a threading issue
occurred while interacting with the treeSQLException
- if an SQLException exception thrown whenever a
problem occurred while interacting with the tree databaseArrayList<PeptideProteinMapping> getProteinMapping(Tag tag, TagMatcher tagMatcher, SequenceMatchingPreferences sequenceMatchingPreferences, Double massTolerance) throws IOException, InterruptedException, ClassNotFoundException, SQLException
tag
- the tag to look for in the tree. Must contain a consecutive
amino acid sequence of longer or equal size than the initialTagSize of
the treetagMatcher
- the tag matcher to usesequenceMatchingPreferences
- the sequence matching preferencesmassTolerance
- the MS2 m/z toleranceIOException
- exception thrown whenever an error occurs while
reading or writing a file.ClassNotFoundException
- exception thrown whenever an error occurs
while deserializing an object.InterruptedException
- exception thrown whenever a threading issue
occurred while interacting with the tree.SQLException
- if an SQLException exception thrown whenever a
problem occurred while interacting with the tree database.ArrayList<PeptideProteinMapping> getProteinMapping(Tag tag, TagMatcher tagMatcher, SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, InterruptedException, ClassNotFoundException, SQLException
tag
- the tag to look for in the tree. Must contain a consecutive
amino acid sequence of longer or equal size than the initialTagSize of
the treetagMatcher
- the tag matcher to usesequenceMatchingPreferences
- the sequence matching preferencesIOException
- exception thrown whenever an error occurs while
reading or writing a file.ClassNotFoundException
- exception thrown whenever an error occurs
while deserializing an object.InterruptedException
- exception thrown whenever a threading issue
occurred while interacting with the tree.SQLException
- if an SQLException exception thrown whenever a
problem occurred while interacting with the tree database.void emptyCache()
void close() throws IOException, SQLException, InterruptedException
IOException
- exception thrown whenever an error occurs while
reading or writing a file.SQLException
- exception thrown whenever a problem occurred while
interacting with a database.InterruptedException
- exception thrown if a threading error occursCopyright © 2018. All rights reserved.